Research workbench

State a architectural model (NSA1-tap flag-YTM1) - visualizing the assembly pathway of nucleolar pre-60S ribosomes

Analyse State a architectural model (NSA1-tap flag-YTM1) - visualizing the assembly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6EM3
Type: protein + RNA
Length: 6,665 residues
Chains: 33
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosome production factor 1; 60S ribosomal protein L7-a; Protein MAK16; Ribosomal…
EC: 3.6.4.13
UniProt: P38805, P05737, P10962, P35178, P53136, Q08235, P36049, P40007, P10664, P38061, Q02326, P05744, P17076, P0CX84, O14455, P49166, Q12690, P36105, P05748, P26784, P05740, P0CX49, P0CX23, P05743, Q03532, P38779, P53261, P53927, P40693, Q04660
Pockets: 20 · best druggability 0.78

Structure

electron microscopy · 33 distinct chains · 35% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
x	Ribosome production factor 1	protein	267	31% helix, 22% strand	P38805
F	60S ribosomal protein L7-a	protein	241	54% helix, 13% strand	P05737
3	Protein MAK16	protein	173	40% helix, 15% strand	P10962
4	Ribosomal RNA-processing protein 1	protein	220	58% helix, 0% strand	P35178
5	Ribosome biogenesis protein NSA1	protein	385	3% helix, 46% strand	P53136
A	Ribosome biogenesis protein BRX1	protein	145	23% helix, 22% strand	Q08235
J	RRNA-processing protein EBP2	protein	66	50% helix, 0% strand	P36049
v	Nucleolar protein 16	protein	130	48% helix, 0% strand	P40007
C	60S ribosomal protein L4-a	protein	343	29% helix, 10% strand	P10664
e	60S ribosomal protein L32	protein	125	19% helix, 11% strand	P38061
E	60S ribosomal protein L6-a	protein	151	23% helix, 20% strand	Q02326
f	60S ribosomal protein L33-a	protein	106	7% helix, 45% strand	P05744
G	60S ribosomal protein L8-a	protein	159	45% helix, 9% strand	P17076
h	60S ribosomal protein L35-a	protein	119	55% helix, 3% strand	P0CX84
i	60S ribosomal protein L36-B	protein	74	78% helix, 0% strand	O14455
j	60S ribosomal protein L37-a	protein	71	23% helix, 8% strand	P49166
L	60S ribosomal protein L13-a	protein	108	44% helix, 13% strand	Q12690
M	60S ribosomal protein L14-a	protein	134	38% helix, 25% strand	P36105
N	60S ribosomal protein L15-a	protein	177	39% helix, 19% strand	P05748
O	60S ribosomal protein L16-a	protein	197	51% helix, 5% strand	P26784
P	60S ribosomal protein L17-a	protein	117	38% helix, 26% strand	P05740
Q	60S ribosomal protein L18-a	protein	131	38% helix, 18% strand	P0CX49
S	60S ribosomal protein L20-a	protein	170	21% helix, 29% strand	P0CX23
Y	60S ribosomal protein L26-a	protein	125	26% helix, 32% strand	P05743
1	25S ribosomal RNA	rna	1250	—	—
2	5.8S ribosomal RNA	rna	157	—	—
D	ATP-dependent RNA helicase HAS1 (EC 3.6.4.13)	protein	194	35% helix, 12% strand	Q03532
K	Proteasome-interacting protein CIC1	protein	246	38% helix, 19% strand	P38779
n	Pescadillo homolog	protein	312	45% helix, 6% strand	P53261
o	Ribosome biogenesis protein 15	protein	116	33% helix, 24% strand	P53927
t	Ribosome biogenesis protein RLP7	protein	248	38% helix, 13% strand	P40693
6	5.8S ribosomal RNA	rna	65	—	—
B	Ribosome biogenesis protein ERB1	protein	143	37% helix, 0% strand	Q04660

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1161	0.78	0.81	122	empty
2	464	0.73	0.83	64	empty
3	716	0.73	0.80	93	empty
4	582	0.72	0.81	80	empty
5	505	0.72	0.82	60	empty

Interfaces

93 interfaces between chains.

C–1 · 2875 Å² buried · 33 hydrogen bonds · protein-nucleic
e–1 · 1499 Å² buried · 17 hydrogen bonds · protein-nucleic
N–1 · 1484 Å² buried · 12 hydrogen bonds · protein-nucleic
1–2 · 1228 Å² buried · 21 hydrogen bonds · nucleic-nucleic
F–1 · 987 Å² buried · 15 hydrogen bonds · protein-nucleic

Compared structures

6EM3 · State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of… · the same entry in another collection · chain E against E, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P38805
Every structure of UniProt P05737
Every structure of UniProt P10962
Every structure of UniProt P35178
Every structure of UniProt P53136
Every structure of UniProt Q08235
Every structure of UniProt P36049
Every structure of UniProt P40007
Every structure of UniProt P10664
Every structure of UniProt P38061
Every structure of UniProt Q02326
Every structure of UniProt P05744
Every structure of UniProt P17076
Every structure of UniProt P0CX84
Every structure of UniProt O14455
Every structure of UniProt P49166
Every structure of UniProt Q12690
Every structure of UniProt P36105
Every structure of UniProt P05748
Every structure of UniProt P26784
Every structure of UniProt P05740
Every structure of UniProt P0CX49
Every structure of UniProt P0CX23
Every structure of UniProt P05743
Every structure of UniProt Q03532
Every structure of UniProt P38779
Every structure of UniProt P53261
Every structure of UniProt P53927
Every structure of UniProt P40693
Every structure of UniProt Q04660
Elsewhere: RCSB PDB 6EM3 · PDBe 6EM3 · UniProt P38805 · UniProt P05737 · UniProt P10962 · UniProt P35178 · UniProt P53136 · UniProt Q08235 · UniProt P36049 · UniProt P40007 · UniProt P10664 · UniProt P38061 · UniProt Q02326 · UniProt P05744 · UniProt P17076 · UniProt P0CX84 · UniProt O14455 · UniProt P49166 · UniProt Q12690 · UniProt P36105 · UniProt P05748 · UniProt P26784 · UniProt P05740 · UniProt P0CX49 · UniProt P0CX23 · UniProt P05743 · UniProt Q03532 · UniProt P38779 · UniProt P53261 · UniProt P53927 · UniProt P40693 · UniProt Q04660

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.